When NOT to trim adaptors?

Question

[rtho]

I can't find much info on this question online, so apologies if it is answered elsewhere. I'm working with whole exome seq data with the aim of identifying somatic variants. Using fastqc I can see adaptor in around 20% of reads by the end of the read (150bp PE).

I always understood that adaptor trimming was routine in this situation but I have seen a few resources recommend against it, without providing any explanation as to why. Can anyone explain why it might be detrimental to trim adaptors prior to alignment?

Thank you

Answer 1

[GenoMax]

It is not detrimental to trim adapters. Reason some people choose not to do it is to save time, especially if you are aligning to a good reference (which you may be doing). Most aligners will soft-clip parts of read that do not align so in theory can take care of any adapter sequences that way. Personally I take the extra time to remove them so I no longer need to think about their presence for any downstream analysis.

[rtho]

Thank you- I only just saw this reply, which is very helpful